Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.3.274-282
D. Strelkova, S. Rachina, V.G. Kuleshov, E. Burmistrova, I. Sychev, N. Ananicheva, Y. Vasileva, E.A. Churkina
Objective. To study spectrum of pathogens and the time to colonization of respiratory samples in patients with severe and critical COVID-19 as well as to analyze incidence of nosocomial infections and structure of prescribed antibacterial drugs. Materials and Methods. The prospective observational study included patients aged 18 years and older with confirmed severe and critical COVID-19 from December 2021 to February 2022. During the first 48 hours and then every 2–3 days of hospitalization, a respiratory sample was collected: sputum, tracheal aspirate (if intubated), bronchoalveolar lavage (if bronchoscopy was performed) for microscopy and microbiological examination. Some patients were screened for invasive aspergillosis. Clinical and demographic data, comorbidities, pathogenetic therapy for COVID-19, antibiotic therapy, cases of probable/documented bacterial nosocomial infections, antibiotic-associated diarrhea, and hospital treatment outcomes were recorded. Results. A total of 82 patients were included in this study. Patients with lung parenchyma involvement of more than 50% by computer tomography predominated; most of them (77%) required intubation and mechanical ventilation due to progression of respiratory failure, and 76% of patients had a lethal outcome. During the first 48 hours, a respiratory sample was obtained from 47 patients; the rest of the patients presented with non-productive cough. No growth of microorganisms was detected in 31 (36.8%) cases; clinically significant pathogens were detected in 16 (19.5%) patients. A subsequent analysis included data from 63 patients with a sufficient number of samples for dynamic observation were used. During the first 3 days of ICU stay, the most common bacterial pathogens were Klebsiella pneumoniae without acquired antibiotic resistance and methicillin-susceptible Staphylococcus aureus. From 3rd day and afterwards, an increase in the proportion of Acinetobacter baumannii, other non-fermenting bacteria, and carbapenemresistant Enterobacterales was noted. Among the pathogens causing lower respiratory tract infections, A. baumannii and carbapenem-resistant K. pneumoniae were predominant pathogens and accounted for 76% of cases. Positive galactomannan test results were obtained in 4 cases. Conclusions. The study confirmed importance of bacterial nosocomial infections in patients with severe and critical COVID-19. In the case of the development of nosocomial lower respiratory tract infections, empirical antimicrobial therapy should take into account the predominance of carbapenem-resistant Enterobacteria and A. baumannii, as well as the possibility of invasive aspergillosis.
{"title":"Microbiological monitoring of COVID-19 patients in the ICU: a prospective observational study","authors":"D. Strelkova, S. Rachina, V.G. Kuleshov, E. Burmistrova, I. Sychev, N. Ananicheva, Y. Vasileva, E.A. Churkina","doi":"10.36488/cmac.2022.3.274-282","DOIUrl":"https://doi.org/10.36488/cmac.2022.3.274-282","url":null,"abstract":"Objective. To study spectrum of pathogens and the time to colonization of respiratory samples in patients with severe and critical COVID-19 as well as to analyze incidence of nosocomial infections and structure of prescribed antibacterial drugs. Materials and Methods. The prospective observational study included patients aged 18 years and older with confirmed severe and critical COVID-19 from December 2021 to February 2022. During the first 48 hours and then every 2–3 days of hospitalization, a respiratory sample was collected: sputum, tracheal aspirate (if intubated), bronchoalveolar lavage (if bronchoscopy was performed) for microscopy and microbiological examination. Some patients were screened for invasive aspergillosis. Clinical and demographic data, comorbidities, pathogenetic therapy for COVID-19, antibiotic therapy, cases of probable/documented bacterial nosocomial infections, antibiotic-associated diarrhea, and hospital treatment outcomes were recorded. Results. A total of 82 patients were included in this study. Patients with lung parenchyma involvement of more than 50% by computer tomography predominated; most of them (77%) required intubation and mechanical ventilation due to progression of respiratory failure, and 76% of patients had a lethal outcome. During the first 48 hours, a respiratory sample was obtained from 47 patients; the rest of the patients presented with non-productive cough. No growth of microorganisms was detected in 31 (36.8%) cases; clinically significant pathogens were detected in 16 (19.5%) patients. A subsequent analysis included data from 63 patients with a sufficient number of samples for dynamic observation were used. During the first 3 days of ICU stay, the most common bacterial pathogens were Klebsiella pneumoniae without acquired antibiotic resistance and methicillin-susceptible Staphylococcus aureus. From 3rd day and afterwards, an increase in the proportion of Acinetobacter baumannii, other non-fermenting bacteria, and carbapenemresistant Enterobacterales was noted. Among the pathogens causing lower respiratory tract infections, A. baumannii and carbapenem-resistant K. pneumoniae were predominant pathogens and accounted for 76% of cases. Positive galactomannan test results were obtained in 4 cases. Conclusions. The study confirmed importance of bacterial nosocomial infections in patients with severe and critical COVID-19. In the case of the development of nosocomial lower respiratory tract infections, empirical antimicrobial therapy should take into account the predominance of carbapenem-resistant Enterobacteria and A. baumannii, as well as the possibility of invasive aspergillosis.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.3.196-201
A. Siniaev, A.O. Grinenko, M. Popova, Y. Rogacheva, A. Spiridonova, Y. Vlasova, A. Smirnova, E. Morozova, K. Lepik, N. Mikhailova, M. D. Vladovskaya, S. Bondarenko, I. Moiseev, A. Kulagin
Objective. To assess the course and outcomes of COVID-19 in recipients of allogeneic and autologous hematopoietic stem cell transplant (HSCT). Materials and Methods. The retrospective study included 44 adult recipients (allogeneic – 33 [75%] and autologous – 11 [25%] of HSCT who diagnosed with COVID-19 after transplantation. Group mostly represented by acute leukemia – 18 (41%) and lymphoma – 10 (22.7%). The median follow-up time since the development of COVID-19 was 231 days (1–818 days), after HSCT – 507.5 days (14–3723 days). Overall and progression-free survival was assessed using the Kaplan–Meier and Log-Rank method. We also evaluated the characteristics of the course of a new coronavirus infection. Results. Median time for the development of COVID-19 from the moment of HSCT was 122.5 days (-1–3490 days). Twelve patients (27.2%) were in grade 3–4 neutropenia at the time of COVID-19 diagnosis, 16 (36.4%) patients were in grade 1–2 neutropenia. Sixteen (48.4%) allo-HSCT recipients had active graft-versus-host disease (GVHD) at the time of COVID-19 development. Disease severity was mild in 19 (43.2%) and moderate in 13 (29.5%) patients. Overall, 200-day survival from the onset of COVID-19 was 78.8% (95% CI [63.1–88.4]). Anemia (p = 0.02) and thrombocytopenia (p = 0.01) significantly decrease OS in patients with COVID-19 after HSCT. Patients with GVHD at the time of COVID-19 onset had a better survival rate (p = 0.02). The timing of COVID-19 development after HSCT did not affect outcomes. Conclusions. The key points of the course of COVID-19 in HSCT recipients are the presence of cytopenia and graft-versus-host disease. Overall survival was 78.8%.
{"title":"COVID-19 infection in hematopoietic stem cell transplant recipients","authors":"A. Siniaev, A.O. Grinenko, M. Popova, Y. Rogacheva, A. Spiridonova, Y. Vlasova, A. Smirnova, E. Morozova, K. Lepik, N. Mikhailova, M. D. Vladovskaya, S. Bondarenko, I. Moiseev, A. Kulagin","doi":"10.36488/cmac.2022.3.196-201","DOIUrl":"https://doi.org/10.36488/cmac.2022.3.196-201","url":null,"abstract":"Objective. To assess the course and outcomes of COVID-19 in recipients of allogeneic and autologous hematopoietic stem cell transplant (HSCT). Materials and Methods. The retrospective study included 44 adult recipients (allogeneic – 33 [75%] and autologous – 11 [25%] of HSCT who diagnosed with COVID-19 after transplantation. Group mostly represented by acute leukemia – 18 (41%) and lymphoma – 10 (22.7%). The median follow-up time since the development of COVID-19 was 231 days (1–818 days), after HSCT – 507.5 days (14–3723 days). Overall and progression-free survival was assessed using the Kaplan–Meier and Log-Rank method. We also evaluated the characteristics of the course of a new coronavirus infection. Results. Median time for the development of COVID-19 from the moment of HSCT was 122.5 days (-1–3490 days). Twelve patients (27.2%) were in grade 3–4 neutropenia at the time of COVID-19 diagnosis, 16 (36.4%) patients were in grade 1–2 neutropenia. Sixteen (48.4%) allo-HSCT recipients had active graft-versus-host disease (GVHD) at the time of COVID-19 development. Disease severity was mild in 19 (43.2%) and moderate in 13 (29.5%) patients. Overall, 200-day survival from the onset of COVID-19 was 78.8% (95% CI [63.1–88.4]). Anemia (p = 0.02) and thrombocytopenia (p = 0.01) significantly decrease OS in patients with COVID-19 after HSCT. Patients with GVHD at the time of COVID-19 onset had a better survival rate (p = 0.02). The timing of COVID-19 development after HSCT did not affect outcomes. Conclusions. The key points of the course of COVID-19 in HSCT recipients are the presence of cytopenia and graft-versus-host disease. Overall survival was 78.8%.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.2.108-133
I. Andreeva, A.V. Tolpygo, V. Andreev, I. S. Azyzov, I. Golman, N. Osipova, V. Privolnev, O. Stetsiouk, V. Sokolovskaya
Psychobiotics are a special class of probiotics that have a beneficial effect on human mental health. During the last decade, convincing evidence has emerged that the gut microbiome influences mental health, cognitive abilities (learning and memory), and behavioral processes through neurological, metabolic, hormonal, and immunological signaling pathways. This review provides available information on the mechanisms of regulation of neuroimmune axes by the microbiota, describes the schemes of interaction of the microbiota with the intestinal nervous system and the brain-gut axis, the effect on behavior, cognitive functions and emotions, and discusses the evidence base and current views on the use of psychobiotics as a safe and effective therapeutic alternative to classic psychotropic drugs in depressive and anxiety disorders, stress, autism spectrum disorders, Alzheimer’s disease and other conditions.
{"title":"Psychobiotics: a new way in psychopharmacology, or How do bacteria manage our brain?","authors":"I. Andreeva, A.V. Tolpygo, V. Andreev, I. S. Azyzov, I. Golman, N. Osipova, V. Privolnev, O. Stetsiouk, V. Sokolovskaya","doi":"10.36488/cmac.2022.2.108-133","DOIUrl":"https://doi.org/10.36488/cmac.2022.2.108-133","url":null,"abstract":"Psychobiotics are a special class of probiotics that have a beneficial effect on human mental health. During the last decade, convincing evidence has emerged that the gut microbiome influences mental health, cognitive abilities (learning and memory), and behavioral processes through neurological, metabolic, hormonal, and immunological signaling pathways. This review provides available information on the mechanisms of regulation of neuroimmune axes by the microbiota, describes the schemes of interaction of the microbiota with the intestinal nervous system and the brain-gut axis, the effect on behavior, cognitive functions and emotions, and discusses the evidence base and current views on the use of psychobiotics as a safe and effective therapeutic alternative to classic psychotropic drugs in depressive and anxiety disorders, stress, autism spectrum disorders, Alzheimer’s disease and other conditions.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69623927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.4.375-382
Y. Rogacheva, M. Popova, A. Siniaev, A. Spiridonova, V. Markelov, Y. Vlasova, S. Bondarenko, L. Zubarovskaya, A. Kulagin
Objective. To study epidemiology and impact of colonization by multidrug-resistant Gram-negative bacteria (MDRGNB) on bloodstream infections (BSI) during allogeneic hematopoietic stem cell transplantation (allo-HSCT). Materials and Methods. The retrospective study included 288 patients received the first allo-HSCT between 2018 and 2019. The median age was 32 (18–66) years, male – 53% (n = 152). The majority of patients had acute leukemia – 62% (n = 178) and received transplant from matched unrelated – 42% (n = 120) or haploidentical donor – 26% (n = 75). Relapse of underlying disease at the moment of all-HSCT was registered in 23% (n = 66) of patients. Results. Colonization of non-sterile sites before allo-HSCT by at least one MDRGNB was detected in 28% (n = 64). In most cases resistance is due to extended spectrum beta-lactamases (ESBL) – 86% (n = 55), while carbapenemases in combination with ESBL were detected in 14% (n = 9) of patients. After allo-HSCT the colonization was significantly higher than before transplantation (n = 161, 56%, p = 0.001), mainly due to carbapenemase- and ESBL-producing bacteria – 73% (n = 118) (p = 0.001). BSI in the early period after transplantation developed in 26% (n = 76), and in 56% (n = 43) was caused by MDRGNB. The etiology of BSI included K. pneumoniae – 51% in mostly cases. The etiology of BSI was the same bacteria that colonized non-sterile sites 2 weeks before the detection bacteria in bloodstream in 69% (n = 30) patients. Colonization by MDRGNB was associated with the development of BSI (p < 0.0001). The 100-day overall survival (OS) after all-HSCT was significantly lower in patients with colonization of non-sterile sites by MDRGNB compared with patients without colonization (60.6% vs 88.2%, p = 0.001). Conclusions. Colonization of MDRGNB after allo-HSCT reached 56%. K. pneumoniae was predominant etiology in both colonization and bloodstream infections. Colonization by MDRGNB was associated with the development of BSI and decreased OS after allo-HSCT.
{"title":"Epidemiology and impact of colonization by multidrug-resistant Gram-negative bacteria on bloodstream infections in early phase of allogeneic hematopoietic stem cell transplantation","authors":"Y. Rogacheva, M. Popova, A. Siniaev, A. Spiridonova, V. Markelov, Y. Vlasova, S. Bondarenko, L. Zubarovskaya, A. Kulagin","doi":"10.36488/cmac.2022.4.375-382","DOIUrl":"https://doi.org/10.36488/cmac.2022.4.375-382","url":null,"abstract":"Objective. To study epidemiology and impact of colonization by multidrug-resistant Gram-negative bacteria (MDRGNB) on bloodstream infections (BSI) during allogeneic hematopoietic stem cell transplantation (allo-HSCT). Materials and Methods. The retrospective study included 288 patients received the first allo-HSCT between 2018 and 2019. The median age was 32 (18–66) years, male – 53% (n = 152). The majority of patients had acute leukemia – 62% (n = 178) and received transplant from matched unrelated – 42% (n = 120) or haploidentical donor – 26% (n = 75). Relapse of underlying disease at the moment of all-HSCT was registered in 23% (n = 66) of patients. Results. Colonization of non-sterile sites before allo-HSCT by at least one MDRGNB was detected in 28% (n = 64). In most cases resistance is due to extended spectrum beta-lactamases (ESBL) – 86% (n = 55), while carbapenemases in combination with ESBL were detected in 14% (n = 9) of patients. After allo-HSCT the colonization was significantly higher than before transplantation (n = 161, 56%, p = 0.001), mainly due to carbapenemase- and ESBL-producing bacteria – 73% (n = 118) (p = 0.001). BSI in the early period after transplantation developed in 26% (n = 76), and in 56% (n = 43) was caused by MDRGNB. The etiology of BSI included K. pneumoniae – 51% in mostly cases. The etiology of BSI was the same bacteria that colonized non-sterile sites 2 weeks before the detection bacteria in bloodstream in 69% (n = 30) patients. Colonization by MDRGNB was associated with the development of BSI (p < 0.0001). The 100-day overall survival (OS) after all-HSCT was significantly lower in patients with colonization of non-sterile sites by MDRGNB compared with patients without colonization (60.6% vs 88.2%, p = 0.001). Conclusions. Colonization of MDRGNB after allo-HSCT reached 56%. K. pneumoniae was predominant etiology in both colonization and bloodstream infections. Colonization by MDRGNB was associated with the development of BSI and decreased OS after allo-HSCT.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.3.254-260
I. S. Azyzov, А.А. Martinovich
Objective. To evaluate the possibility of using the colistin disk chelator application (CDCA) method as simple and available screening tool for detection of mcr-1-mediated resistance to polymyxins in Enterobacterales. Materials and Methods. A total of 47 colistin-resistant Enterobacterales isolates obtained in 2014–2020 within multicenter MARATHON study were included in the experiment. Colistin susceptibility testing was performed using Mueller–Hinton broth microdilution method according to ISO 20776-1:2006. Interpretation of the results was performed according to EUCAST v.12.0 clinical breakpoints. MCR-genes were detected by multiplex real-time PCR. Phenotypic screening for mcr-expression was performed on Mueller–Hinton agar by application of dipicolinic acid in concentration of 1,000 mcg/disk in 10 µL volume per disk and 0.5 M solution of EDTA in 5 µL volume per disk. Chelating effect was registered by differences in zone of growth inhibition around colistin disks with and without chelator. Measurements were performed with the help of caliper in millimeters. Statistical data processing was carried out in accordance with guidelines for statistical analysis in medical researches using MS-Excel tool. Results. In 25 of 47 included in the experiment enterobacteria isolates mcr-genes were detected by molecular method. MCR-detection by CDCA method identified the average difference value of the zones of growth inhibition for colistin and its combination with EDTA and DPA as 4.1 mm and 3.7 mm respectively for mcr-positive isolates and 1.7 mm and 1.2 mm respectively for mcr-negative isolates. Statistical analysis estimated that a difference of ≥ 3 mm in zone of growth inhibition for combination of colistin with one of the chelating agents when compared to colistin only allows us to conclude that a studied isolated carries mcr-1-mediated resistance to polymyxins. In addition, sensitivity of the test was 96% and specificity was 91% if DPA is used, while EDTA showed only 88% sensitivity and 77% specificity. Conclusions. Proposed method appears as available technique for phenotypic screening of the Enterobacterales order for mcr-1-mediated resistance to polymyxins for practical laboratories in present conditions. The use of DPA is preferred because of better specificity and sensitivity rates.
{"title":"Detection of mcr-1-mediated resistance to polymyxins in Enterobacterales using colistin disk chelator application","authors":"I. S. Azyzov, А.А. Martinovich","doi":"10.36488/cmac.2022.3.254-260","DOIUrl":"https://doi.org/10.36488/cmac.2022.3.254-260","url":null,"abstract":"Objective. To evaluate the possibility of using the colistin disk chelator application (CDCA) method as simple and available screening tool for detection of mcr-1-mediated resistance to polymyxins in Enterobacterales. Materials and Methods. A total of 47 colistin-resistant Enterobacterales isolates obtained in 2014–2020 within multicenter MARATHON study were included in the experiment. Colistin susceptibility testing was performed using Mueller–Hinton broth microdilution method according to ISO 20776-1:2006. Interpretation of the results was performed according to EUCAST v.12.0 clinical breakpoints. MCR-genes were detected by multiplex real-time PCR. Phenotypic screening for mcr-expression was performed on Mueller–Hinton agar by application of dipicolinic acid in concentration of 1,000 mcg/disk in 10 µL volume per disk and 0.5 M solution of EDTA in 5 µL volume per disk. Chelating effect was registered by differences in zone of growth inhibition around colistin disks with and without chelator. Measurements were performed with the help of caliper in millimeters. Statistical data processing was carried out in accordance with guidelines for statistical analysis in medical researches using MS-Excel tool. Results. In 25 of 47 included in the experiment enterobacteria isolates mcr-genes were detected by molecular method. MCR-detection by CDCA method identified the average difference value of the zones of growth inhibition for colistin and its combination with EDTA and DPA as 4.1 mm and 3.7 mm respectively for mcr-positive isolates and 1.7 mm and 1.2 mm respectively for mcr-negative isolates. Statistical analysis estimated that a difference of ≥ 3 mm in zone of growth inhibition for combination of colistin with one of the chelating agents when compared to colistin only allows us to conclude that a studied isolated carries mcr-1-mediated resistance to polymyxins. In addition, sensitivity of the test was 96% and specificity was 91% if DPA is used, while EDTA showed only 88% sensitivity and 77% specificity. Conclusions. Proposed method appears as available technique for phenotypic screening of the Enterobacterales order for mcr-1-mediated resistance to polymyxins for practical laboratories in present conditions. The use of DPA is preferred because of better specificity and sensitivity rates.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.1.61-66
A.N. Chagaryan, N. Ivanchik, K. Mironov, A. Muravyev
Pneumococcal conjugate vaccines contain a limited number of serotype-specific antigens of S. pneumoniae. It is important for vaccination programmes effectiveness assessment to control a variety of circulating S. pneumoniae serotypes. This review provides an analysis of pneumococcal serotyping approaches and further ways of improving pneumococcal serotype detection within the microbiological surveillance. Serological methods and multiplex PCR can identify a limited number of pneumococcal serotypes only. Whole-genome sequencing-based approaches can predict almost all serotypes and sequence types as well as detect antimicrobial resistance and virulence genes.
{"title":"Current methods of capsular typing of Streptococcus pneumoniae: possibilities and availability for local laboratories","authors":"A.N. Chagaryan, N. Ivanchik, K. Mironov, A. Muravyev","doi":"10.36488/cmac.2022.1.61-66","DOIUrl":"https://doi.org/10.36488/cmac.2022.1.61-66","url":null,"abstract":"Pneumococcal conjugate vaccines contain a limited number of serotype-specific antigens of S. pneumoniae. It is important for vaccination programmes effectiveness assessment to control a variety of circulating S. pneumoniae serotypes. This review provides an analysis of pneumococcal serotyping approaches and further ways of improving pneumococcal serotype detection within the microbiological surveillance. Serological methods and multiplex PCR can identify a limited number of pneumococcal serotypes only. Whole-genome sequencing-based approaches can predict almost all serotypes and sequence types as well as detect antimicrobial resistance and virulence genes.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69623825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.3.226-235
N. Karoli, A. Rebrov
Currently, there is a lack of evidence for empiric use of antimicrobial agents in most patients with COVID-19 in outpatient and hospital settings as the overall proportion of secondary bacterial infections in COVID-19 is quite low. This literature review summarizes data on changes in antimicrobial resistance over the course of COVID-19 pandemic, especially in nosocomial ESKAPE pathogens. The other significant consequences of excessive and unnecessary administration of antibiotics to COVID-19 patients including risk of Clostridioides difficile infection and adverse effects of antimicrobial agents are also discussed.
{"title":"Some issues of safety of antimicrobial therapy in COVID-19 patients","authors":"N. Karoli, A. Rebrov","doi":"10.36488/cmac.2022.3.226-235","DOIUrl":"https://doi.org/10.36488/cmac.2022.3.226-235","url":null,"abstract":"Currently, there is a lack of evidence for empiric use of antimicrobial agents in most patients with COVID-19 in outpatient and hospital settings as the overall proportion of secondary bacterial infections in COVID-19 is quite low. This literature review summarizes data on changes in antimicrobial resistance over the course of COVID-19 pandemic, especially in nosocomial ESKAPE pathogens. The other significant consequences of excessive and unnecessary administration of antibiotics to COVID-19 patients including risk of Clostridioides difficile infection and adverse effects of antimicrobial agents are also discussed.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.4.292-294
A. Veselov
{"title":"Changes in the nomenclature of human pathogenic micromycetes","authors":"A. Veselov","doi":"10.36488/cmac.2022.4.292-294","DOIUrl":"https://doi.org/10.36488/cmac.2022.4.292-294","url":null,"abstract":"","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.2.171-179
A. Malchikova, G. Klyasova
Objective. To present the results of using in-house method for rapid identification of fungi from funguspositive bottles with routine conventional culture-based identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in patients with bloodstream infection. Materials and Methods. Prospective study was performed from 2016 to 2019 at the National Research Center for Hematology, Moscow. During the study period, all blood cultures (BC) bottles obtained from hematological patients were incubated in the BACTEC FX system (Becton Dickinson, USA). Positive BC bottles were examined by Gram stain. In house method was used after Gram stain was positive for yeast cells or hyphae. For that, BC media was transfer from fungus-positive bottles into tube. In house method included series section steps consisted from centrifugation and extraction of fungal proteins by adding of sodium dodecyl sulfate. Routine conventional culture-based identification on Sabouraud with chloramphenicol agar (bioMerieux, France) for yeasts and on Sabouraud dextrose agar (Oxoid, UK) for molds was used simultaneously with the in house method. Results. During the study period, 16 fungus-positive bottles were obtained from which were isolated in monoculture 14 (87.5%) Candida spp.: C. parapsilosis (n = 5), C. tropicalis (n = 4), C. albicans (n = 3), C. krusei (n = 1), C. guilliermondii (n = 1), one (6.3%) Rhodotorula mucilaginosa and one (6.3%) Fusarium dimerum. The in house method resulted in 75% (12⁄16) and 68.8% (11⁄16) identification rate at the genus and species level of fungi, respectively. The identification of fungi to species level was confirmed by conventional culture-based method in all cases. The median time from the start of vial incubation in BACTEC FX system to identification of fungi by in house method was less than conventional culture-based identification: 36 hrs 20 min vs 55 hrs 31 min (p = 0.028). Conclusions. A high rate of correct direct species identification and significant reduction in time to verification of fungi from fungus-positive bottles by in house method were obtained. The proposed in house method should be recommended for use in real microbiology practice to reduce the time for submitting results of identification to clinical units.
{"title":"In house method for rapid identification of fungi from fungus-positive bottles by MALDI-TOF mass spectrometry in patients with bloodstream infection","authors":"A. Malchikova, G. Klyasova","doi":"10.36488/cmac.2022.2.171-179","DOIUrl":"https://doi.org/10.36488/cmac.2022.2.171-179","url":null,"abstract":"Objective. To present the results of using in-house method for rapid identification of fungi from funguspositive bottles with routine conventional culture-based identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in patients with bloodstream infection. Materials and Methods. Prospective study was performed from 2016 to 2019 at the National Research Center for Hematology, Moscow. During the study period, all blood cultures (BC) bottles obtained from hematological patients were incubated in the BACTEC FX system (Becton Dickinson, USA). Positive BC bottles were examined by Gram stain. In house method was used after Gram stain was positive for yeast cells or hyphae. For that, BC media was transfer from fungus-positive bottles into tube. In house method included series section steps consisted from centrifugation and extraction of fungal proteins by adding of sodium dodecyl sulfate. Routine conventional culture-based identification on Sabouraud with chloramphenicol agar (bioMerieux, France) for yeasts and on Sabouraud dextrose agar (Oxoid, UK) for molds was used simultaneously with the in house method. Results. During the study period, 16 fungus-positive bottles were obtained from which were isolated in monoculture 14 (87.5%) Candida spp.: C. parapsilosis (n = 5), C. tropicalis (n = 4), C. albicans (n = 3), C. krusei (n = 1), C. guilliermondii (n = 1), one (6.3%) Rhodotorula mucilaginosa and one (6.3%) Fusarium dimerum. The in house method resulted in 75% (12⁄16) and 68.8% (11⁄16) identification rate at the genus and species level of fungi, respectively. The identification of fungi to species level was confirmed by conventional culture-based method in all cases. The median time from the start of vial incubation in BACTEC FX system to identification of fungi by in house method was less than conventional culture-based identification: 36 hrs 20 min vs 55 hrs 31 min (p = 0.028). Conclusions. A high rate of correct direct species identification and significant reduction in time to verification of fungi from fungus-positive bottles by in house method were obtained. The proposed in house method should be recommended for use in real microbiology practice to reduce the time for submitting results of identification to clinical units.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-01-01DOI: 10.36488/cmac.2022.4.314-344
V. Chernyshov, A. Kuzovlev, N.D. Cherepanova, M. A. Kasatkina, R. Ivanov
Due to uncontrolled growth of antimicrobial resistance, in the near future humanity may return to the «pre-antibiotic era» with no reliable antimicrobial therapy even for previously easily treatable infectious diseases. One of possible solutions is improved delivery of antibiotics to antibiotic-resistant bacterial strains by conjugating them with siderophores (small molecules secreted by microorganisms to absorb essential Fe(III)). The siderophore-modified antibiotic (sideromycin), like a Trojan horse, permeates the bacterial cell as a complex with Fe(III), allowing the antibiotic to reach its biological target. In this review, we describe the structural diversity of siderophore-antibiotic conjugates with the focus on the structure of sideromycin as well as on the relationship between the structure of sideromycin and its antibacterial activity. We analyze main representatives of various classes of siderophores; the structural diversity of sideromycins and their antibacterial activity discussed in detail.
{"title":"Siderophore‑antibiotic conjugates: structural diversity and antibacterial activity","authors":"V. Chernyshov, A. Kuzovlev, N.D. Cherepanova, M. A. Kasatkina, R. Ivanov","doi":"10.36488/cmac.2022.4.314-344","DOIUrl":"https://doi.org/10.36488/cmac.2022.4.314-344","url":null,"abstract":"Due to uncontrolled growth of antimicrobial resistance, in the near future humanity may return to the «pre-antibiotic era» with no reliable antimicrobial therapy even for previously easily treatable infectious diseases. One of possible solutions is improved delivery of antibiotics to antibiotic-resistant bacterial strains by conjugating them with siderophores (small molecules secreted by microorganisms to absorb essential Fe(III)). The siderophore-modified antibiotic (sideromycin), like a Trojan horse, permeates the bacterial cell as a complex with Fe(III), allowing the antibiotic to reach its biological target. In this review, we describe the structural diversity of siderophore-antibiotic conjugates with the focus on the structure of sideromycin as well as on the relationship between the structure of sideromycin and its antibacterial activity. We analyze main representatives of various classes of siderophores; the structural diversity of sideromycins and their antibacterial activity discussed in detail.","PeriodicalId":53392,"journal":{"name":"Klinicheskaia mikrobiologiia i antimikrobnaia khimioterapiia","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69624592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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